He was on the side of toleration and protected the reformers.
Religious toleration was granted, but with the important exception that some harsh measures were enacted against Anglicans and Roman Catholics, to neither of whom was liberty of worship accorded.
Complete toleration in fact was only extended to Protestant nonconformists, who composed the Cromwellian established church, and who now meted out to their antagonists the same treatment which they themselves were later to receive under the Clarendon Code of Charles II.
In 1646 appeared his famous plea for toleration, eeoXoyia 'EKXEKTLKii, A Discourse of the Liberty of Prophesying.
The manner in which those who separated themselves from the church were to be dealt with, and the amount of toleration which should be accorded to meetings held in private houses for the purpose of religious edification.